The nation's most powerful doctors' group has thrown its weight behind same-sex marriage for the first time, declaring it a public health issue and calling on politicians to end the divisive debate.

After a 14-year internal tussle, the Australian Medical Association will on Saturday issue a new policy position paper that states excluding same-sex couples from marriage has significant mental and physical health consequences and contributes to high suicide rates in the gay community.

In an unprecedented move, the president of the typically conservative group, Dr Michael Gannon, has written to Prime Minister Malcolm Turnbull and Opposition Leader Bill Shorten urging bipartisanship.

"Discrimination has a severe, damaging impact on mental and physiological health outcomes and LGBTIQ individuals have endured a long history of institutional discrimination in this country," Dr Gannon said.

"Many of these inequalities have been rightly nullified. Homosexuality is no longer a crime, nor is it classified as a psychiatric disorder. The 'gay panic' defence is no longer allowed in cases of murder or assault and same-sex couples are allowed to adopt children in most jurisdictions.

"However, LGBTIQ-identifying Australians will not enjoy equal treatment under Australian law until they can marry."

The AMA's move will put renewed pressure on Mr Turnbull to stare down the right-wing of his party and allow a free vote in the Parliament. While Mr Turnbull personally supports a free vote, Coalition policy remains to hold a public plebiscite - even though the Parliament has blocked that plan.

Dr Gannon said the prolonged, divisive public debate about marriage equality had damaging effects and the Parliament should legislate for same-sex marriage as soon as possible.

The AMA's "groundbreaking" paper is the culmination of a long fight for high-profile Sydney physician and campaigner Kerryn Phelps.

Professor Phelps became the inadvertent early figurehead of the same-sex marriage movement when she was publicly outed by the media in 1998, shortly after she travelled overseas to marry her partner Jackie Stricker.

Two years later, she was elected head of the AMA - the first woman and first gay person to fill the role. It was then she started the battle to have sexuality and gender diversity recognised as a health issue.

"The political and legislative support for the security of family groups is a very conservative ideal," said Prof Phelps, who was made a Member of the Order of Australia for her services to medicine.

"I don't think the religious, cultural right-wing conservatives now have anywhere to hide. There is no excuse for delaying this any further. The medical profession has carefully considered the health consequences of continued discrimination and made an emphatic statement that it should end.

"I think politicians now have a duty of care to the community to make sure marriage equality is introduced as soon as possible."

People who identify as gay or transgender have significantly poorer mental and physiological health outcomes than those experienced by the broader population, the AMA's paper notes. They are more likely to engage in high-risk behaviour such as illicit drug use or alcohol abuse and have the highest rates of suicide in Australia.

It points to "minority stress" caused by a hostile of homophobic culture as a major contributor to poor mental health.

The lack of legal recognition can also have tragic consequences in medical emergencies as a partner may not have the right to advocate for their ill or injured partner. In these circumstances decision-making may be deferred to a member of the patient's biological family instead.

Under the new policy, the AMA also wants anti-discrimination laws maintained and enforced to ensure businesses cannot withhold goods or services from clients due to their gender or sexual orientation.

The paper says there is "no putative, peer-reviewed evidence to suggest that children raised in same-sex parented families suffer poorer health or psychosocial outcomes as a direct result of the sexual orientation of their parents or carers".

"Children of same-sex parented families do, however, experience negative psychosocial outcomes when their family is the subject of perceived stigmatisation, rejection, or homophobia," it says.

Alex Greenwich from Australian Marriage Equality called the move "extremely significant" and hopes it will change the political conversation.

"The AMA is an organisation with conservative views," he said.

"If the AMA can come out and support marriage equality - after having quite a long-term conversation about it internally - then of course the Coalition government should be able to do the same."